The purpose of this study was to investigate micro-morphology of the resin-dentin inter-diffusion zone using two different single-bottle self-etching dentin adhesives with and without previous acid-etching, after in vitro mechanical loading stimuli. Extracted human third molars were sectioned to obtain dentin surfaces. Two different single-bottle self-etching dentin adhesives, Futurabond U and Experimental both from VOCO, were applied following the manufacturer’s instructions or after 37% phosphoric acid application. Resin-dentin interfaces were analyzed with dye assisted confocal microscopy evaluation (CLSM), including the calcium-chelation technique, xylenol orange (CLSM-XO). CLSM revealed that resin-dentin interfaces of unloaded specimens were deficiently resin-hybridized, in general. These samples showed a Rhodamine B-labeled hybrid complex and adhesive layer completely affected by fluorescein penetration (nanoleakage) through the porous resin-dentin interface, but thicker after PA-etching. Load cycling promoted an improved sealing of the resin-dentin interface at dentin, a decrease of the hybrid complex porosity, and an increment of dentin mineralization. Load cycled specimens treated with the XO technique produced a clearly outlined fluorescence due to consistent Ca-mineral deposits within the bonding interface and inside the dentinal tubules, especially when the experimental adhesive was applied.